CCLE_integrative

Integrating CCLE RNA-seq and RPPA data.

Data using:

1. raw RNA-seq gene counts*
2. TPM normalized RNA-seq*
3. RPKM normalized RNA-seq
4. normalized RPPA*

• Used these datasets for analysis

Data was obtained from CCLE: https://portals.broadinstitute.org/ccle

Names of datasets used (based on v3.1 script):

1. CCLE_RNAseq_genes_counts_20180929.gct (found in CCLE site)

   • Raw RNA-seq counts
   • used for PCA

2. CCLE_RNAseq_rsem_genes_tpm_20180929.txt (found in CCLE site)

   • RNA-seq counts TPM normalized

3. breast_cell_lines_V2.csv (found in metadata folder in github)

   • breast cancer cell lines only
   • ER positive vs. negative metadata

4. CCLE_RPPA_20181003.csv (found in CCLE site)

   • RPPA data
   • log2 median-centered
   • for more info: https://www.mdanderson.org/content/dam/mdanderson/documents/core-facilities/Functional%20Proteomics%20RPPA%20Core%20Facility/RPPA%20Materials_Methods_2016.pdf

5. CCLE_RPPA_Ab_info_20181226.csv (found in CCLE site)

   • RPPA antibody/gene data

Folders in github that are relevant:

1. comparison_plots_081420
   • plots that compare integrative vs. RNA-seq only pathways
2. int_080320
   • plots for integrative pathways
3. rna_only_080320
   • plots for RNA-seq only pathways
4. scripts
   • R code (use the most current one: v3.1)
5. metadata
   • extra metadata sets
6. presentations
   • presentations on methods and results
7. lm_FC
   • plots for linear model transformation